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- PDB-2af4: Phosphotransacetylase from Methanosarcina thermophila co-crystall... -

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Basic information

Entry
Database: PDB / ID: 2af4
TitlePhosphotransacetylase from Methanosarcina thermophila co-crystallized with coenzyme A
ComponentsPhosphate acetyltransferase
KeywordsTRANSFERASE / Pta dimer with one CoA ligand bound per monomer / acyltransferase
Function / homology
Function and homology information


phosphate acetyltransferase activity / phosphate acetyltransferase / acetyl-CoA biosynthetic process / plasma membrane
Similarity search - Function
Isocitrate/Isopropylmalate dehydrogenase-like / Rossmann fold - #10950 / Phosphate acetyltransferase / Phosphate acetyl/butyryltransferase / Phosphate acetyltransferase, domain 2 / Phosphate acetyltransferase, domain 1 / Phosphate acetyl/butaryl transferase / Phosphate acetyl/butaryl transferase / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
COENZYME A / Phosphate acetyltransferase
Similarity search - Component
Biological speciesMethanosarcina thermophila (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.147 Å
AuthorsLawrence, S.H. / Luther, K.B. / Ferry, J.G. / Schindelin, H.
Citation
Journal: J.Bacteriol. / Year: 2006
Title: Structural and functional studies suggest a catalytic mechanism for the phosphotransacetylase from Methanosarcina thermophila.
Authors: Lawrence, S.H. / Luther, K.B. / Schindelin, H. / Ferry, J.G.
#1: Journal: Structure / Year: 2004
Title: Crystal structure of phosphotransacetylase from the methanogenic archaeon Methanosarcina thermophila
Authors: Iyer, P.P. / Lawrence, S.H. / Luther, K.B. / Rajashankar, K.R. / Yennawar, H.P. / Ferry, J.G. / Schindelin, H.
History
DepositionJul 25, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 24, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 23, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C: Phosphate acetyltransferase
D: Phosphate acetyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,0824
Polymers70,5472
Non-polymers1,5352
Water4,900272
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5540 Å2
ΔGint-28 kcal/mol
Surface area27010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)116.488, 116.488, 127.460
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number80
Space group name H-MI41

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Components

#1: Protein Phosphate acetyltransferase / Phosphotransacetylase


Mass: 35273.492 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanosarcina thermophila (archaea) / Gene: pta / Plasmid: pT7-7 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P38503, phosphate acetyltransferase
#2: Chemical ChemComp-COA / COENZYME A


Mass: 767.534 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H36N7O16P3S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 272 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.08 Å3/Da / Density % sol: 59.75 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: sodium citrate, HEPES, Coenzyme A, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X26C / Wavelength: 1.1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Aug 29, 2004 / Details: doubly focusing toroidal mirror
RadiationMonochromator: Si 111 channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.147→20 Å / Num. all: 46290 / Num. obs: 45391 / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.2 % / Rmerge(I) obs: 0.066 / Rsym value: 0.066 / Net I/σ(I): 24
Reflection shellResolution: 2.147→2.19 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.427 / Mean I/σ(I) obs: 2.38 / Rsym value: 0.427 / % possible all: 99.2

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1QZT

1qzt


Resolution: 2.147→20 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.923 / SU B: 14.715 / SU ML: 0.196 / Cross valid method: THROUGHOUT / ESU R: 0.22 / ESU R Free: 0.21 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27228 2356 5.2 %RANDOM
Rwork0.20297 ---
obs0.20646 43035 98.06 %-
all-46290 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 60.125 Å2
Baniso -1Baniso -2Baniso -3
1--1.24 Å20 Å20 Å2
2---1.24 Å20 Å2
3---2.49 Å2
Refinement stepCycle: LAST / Resolution: 2.147→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4918 0 96 272 5286
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0225086
X-RAY DIFFRACTIONr_bond_other_d0.0030.024756
X-RAY DIFFRACTIONr_angle_refined_deg1.7612.0096901
X-RAY DIFFRACTIONr_angle_other_deg0.9311117
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1585661
X-RAY DIFFRACTIONr_dihedral_angle_2_deg43.06426.111180
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.49915880
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.8481514
X-RAY DIFFRACTIONr_chiral_restr0.0960.2823
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.025565
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02871
X-RAY DIFFRACTIONr_nbd_refined0.2410.21358
X-RAY DIFFRACTIONr_nbd_other0.1930.25329
X-RAY DIFFRACTIONr_nbtor_refined0.1820.22496
X-RAY DIFFRACTIONr_nbtor_other0.0890.23150
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2370.2303
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.1050.22
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1640.211
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2140.244
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1510.210
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8371.54206
X-RAY DIFFRACTIONr_mcbond_other0.1851.51344
X-RAY DIFFRACTIONr_mcangle_it1.09125294
X-RAY DIFFRACTIONr_scbond_it2.01232011
X-RAY DIFFRACTIONr_scangle_it3.1264.51607
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.147→2.202 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.349 182 -
Rwork0.284 3018 -
obs--94.76 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.77780.60740.24414.37330.9241.99160.07750.2897-0.2733-0.60350.1342-0.46360.03410.1847-0.21160.09110.0736-0.1747-0.0485-0.1861-0.167134.17231.6075-12.8142
22.0106-0.87820.09995.6959-0.67213.16260.15-0.0919-0.01850.09020.2980.13970.12270.2866-0.4479-0.3508-0.0193-0.2081-0.3002-0.0193-0.335729.191755.27086.4434
35.62381.5215-4.97266.22261.82327.8304-0.01260.2908-0.0751-1.22880.1823-0.65890.02170.3845-0.1696-0.00740.0528-0.2079-0.1607-0.1584-0.227436.311241.2272-8.122
46.2747-1.1099-1.22287.34752.17034.6610.1026-1.80510.56511.32770.04890.2567-0.59120.0242-0.15150.2376-0.01850.00620.39220.00740.1810.02789.2714.0973
54.0771-1.57180.0937.5698-2.00634.23640.19560.3366-0.4361-1.17690.40991.43880.4373-0.2747-0.6055-0.1955-0.0724-0.3705-0.25480.15180.006614.976466.2521-6.7121
63.7721-1.4505-3.793619.24941.92714.6782-0.1531-1.12250.17090.88750.57850.0628-0.61490.3069-0.4255-0.1851-0.00410.0068-0.04940.1959-0.050414.634183.94146.1213
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1CA2 - 1502 - 150
2X-RAY DIFFRACTION2CA151 - 295151 - 295
3X-RAY DIFFRACTION3CA296 - 333296 - 333
4X-RAY DIFFRACTION4DB2 - 1502 - 150
5X-RAY DIFFRACTION5DB151 - 295151 - 295
6X-RAY DIFFRACTION6DB296 - 332296 - 332

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